HHsearch alignment for GI: 254780610 and conserved domain: cd00506

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.38  E-value=0.00035  Score=44.69  Aligned_cols=69  Identities=25%  Similarity=0.361  Sum_probs=48.8

Q ss_pred             EEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf             27899624011104567875421002222221024433444436432444433232405721203578888999997211
Q gi|254780610|r   98 DIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGK  177 (340)
Q Consensus        98 ~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~  177 (340)
T Consensus         1 Gil~i~KP~G~TS~--------~vv~~vk~~~~--------~kKvGH~GTLDP~AtGvL~i~vG~a--TK~~~~~~~---   59 (210)
T cd00506           1 GLFAVDKPQGPSSH--------DVVDTIRRIFL--------AEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA---   59 (210)
T ss_pred             CEEEEECCCCCCHH--------HHHHHHHHHHC--------CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC---
T ss_conf             98999679999989--------99999999858--------7735768666974524289997788--879998755---


Q ss_pred             CCCEEEEEEEEEE
Q ss_conf             3221334454320
Q gi|254780610|r  178 STRLKRAYYAMVW  190 (340)
Q Consensus       178 ~~~v~K~Y~Aiv~  190 (340)
T Consensus        60 ---~~K~Y~~~~~   69 (210)
T cd00506          60 ---ATKDYTAIGR   69 (210)
T ss_pred             ---CCCEEEEEEE
T ss_conf             ---9977879999